Circos Methanocatella gottschalkii HO-edt

Methanocatella gottschalkii HO

2026-10-27T23:02:08Z

Heryakusuma:

== Introduction ==
''Methanocatella gottschalkii'' HOT (formerly ''Methanobrevibacter gottschalkii'') is a type strain isolated from the enrichment of horse faeces<ref>Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.</ref>. ''M. gottschalkii'', along with ''Methanobrevibacter ruminantium'', comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets<ref>Henderson, G., Cox, F., Ganesh, S. ''et al.'' Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. ''Sci Rep'' '''5''', 14567 (2015). https://doi.org/10.1038/srep14567. </ref>. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens.

== Global Methane Hub Metadata ==
{| class="wikitable"
!style="text-align: left;"|'''Origin:'''
|Leibniz Institute DSMZ, Germany
|-
!style="text-align: left;"|'''Sequenced by:'''
|Plasmidsaurus, ONT sequencing
|-
!style="text-align: left;"|'''Assembled by:'''
|Christian Heryakusuma
|-
!style="text-align: left;"|'''Methylome called by:'''
|William G. Alexander
|-
!style="text-align: left;"|'''Methyltransferases cloned by:'''
|Guss Lab, ORNL
|-
!style="text-align: left;"|'''MIC and Culturing Conditions by:'''
|Christian Heryakusuma
|-
!style="text-align: left;"|'''Transformation by:'''
|
|}
'''''Abbreviation:''''' ONT, Oxford Nanopore Technologies; ORNL, Oak Ridge National Laboratory.

== Genome ==
{| class="wikitable" style="float: left; margin-right: 2em;"
|+
! colspan="2" |Assembly Summary
|-
|Completeness
|99.97%
|-
|Contamination
|0.16%
|-
|Total contigs
|1
|-
|Max contig length
|1,887,794 bp
|-
|GC content
|30.07%
|}
{| class="wikitable" style="float: left;"
|+
! colspan="2" |Annotation Summary
|-
|Coding density
|88.1%
|-
|tRNAs
|33
|-
|tmRNAs
|0
|-
|rRNAs
|7
|-
|ncRNAs
|1
|-
|ncRNAs regions
|1
|-
|CRISPR arrays
|0
|-
|CDSs
|1847
|-
|Pseudogenes
|2
|-
|Hypotheticals
|1585
|-
|sORFs
|0
|-
|Gaps
|0
|-
|oriCs
|0
|-
|oriVs
|0
|-
|oriTs
|0
|}
<div style="clear: both;"></div>

Genomic DNA (gDNA) of ''M. gottschalkii'' HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch® Spin gDNA Extraction Kit following manufacturer protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with phage pseudomurein endoisopeptidase of ''Methanocatella smithii'' PS (PeiS); an ''Escherichia coli'' strain encoding the PeiS gene was kindly provided by Prof. Metcalf (University of Illinois Urbana-Champaign).

The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.

== Methylome ==

=== Methylation pattern ===
{| class="wikitable"
|+
!'''#motif'''
!'''methylCounts'''
!'''totalCounts'''
!'''%motifsMethyl'''
|-
|C(6mA)YNNNNNRTTG
| align="right" |1495
| align="right" |1558
| align="right" |95.96
|-
|CA(6mA)YNNNNNRTG
| align="right" |1522
| align="right" |1558
| align="right" |97.69
|}
Methylation motifs were analyzed using MIJAMP<ref>Alyssa K Tidwell, Evelyn Faust, Carrie A Eckert, Adam M Guss, William G Alexander, Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP, ''Journal of Industrial Microbiology and Biotechnology'', Volume 52, 2025, kuaf022, https://doi.org/10.1093/jimb/kuaf022. </ref>. 4mC and 5mC motifs were not present in this isolate.

=== DefenseFinder Results ===
add here

=== Methylating ''E. coli'' ===
''E. coli'' strain AG21365 developed by ORNL was used as a host to generate plasmids with ''M. gottschalkii'' HO methylation motifs shown above.

== Culturing Conditions ==
''M. gottschalkii'' HO is cultivated in GMH-VT2 medium at 37°C and 50 rpm with a 30 psig gas mixture of H2:CO2 (80:20, v/v) as an energy substrate. Growth is typically observed within 24 to 48 h. This methanogen can also be cultivated on GMH-VT2 plates using 1.5% gelrite or 2% agar as a gelling agent with a 12 to 30 psig H2:CO2 (80:20, v/v) gas mixture as an energy substrate. Visible growth on plate is usually observable within 2 to 5 days. The viability of ''M. gottschalkii'' HO on agar plates is 10-30 times higher than that of those grown on gelrite plates.

== Antimicrobial MIC Tests ==
[[File:Antimicrobial MIC Tests - M. gottschalkii HO.png|thumb|395x395px|Antimicrobial susceptibility tests on ''M. gottschalkii'' HO'''. Source:''' Christian Heryakusuma.]]

{| class="wikitable"
|+
! rowspan="2" |Antibiotics
! colspan="2" |Concentration
! rowspan="2" |Observation Period
|-
!style="text-align: center;" |'''Liquid'''
!style="text-align: center;" |'''Solid'''
|-
|Sodium sulfite
|0.5 mM
|0.3 mM
|style="text-align: center;" | ~240 h
|-
|Mevinolin
|40 μM
|20 μM
|style="text-align: center;" | ~240 h
|-
|5-fluoroorotic acid (5-FOA)
|style="color: red;"| ''Insensitive''
|style="color: red;"| ''Insensitive''
|style="text-align: center;" | ~240 h
|-
|8-azahypoxanthine (8-AH)
|style="color: red;"| ''Insensitive''
|style="color: red;"| ''Insensitive''
|style="text-align: center;" | ~240 h
|-
|6-mercaptopurine (6-MP)
|style="color: red;"| ''Insensitive''
|style="color: red;"| ''Insensitive''
|style="text-align: center;" | ~240 h
|-
|5-fluorouracil (5-FU)
|0.25 mg/mL
|0.15 mg/mL
|style="text-align: center;" | ~240 h
|-
|Sodium 2-bromoethanesulfonate (BES)
|2 mM
|1 mM
|style="text-align: center;" | ~240 h
|}

Susceptibility testing was evaluated in GMH-VT2 medium inoculated with a 4% ''M. gottschalkii'' HO culture that has a starting OD600 of ~0.4. ''M. gottschalkii'' HO was considered sensitive to the selection or counterselection agents if there was no increase in the OD600 during the ~240 h (10 days) observation period.

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==

Methanocatella gottschalkii HO

2026-10-27T22:57:59Z

Heryakusuma: /* Antimicrobial MIC Tests */

== Introduction ==
''Methanocatella gottschalkii'' HOT (formerly ''Methanobrevibacter gottschalkii'') is a type strain isolated from the enrichment of horse faeces<ref>Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.</ref>. ''M. gottschalkii'', along with ''Methanobrevibacter ruminantium'', comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets<ref>Henderson, G., Cox, F., Ganesh, S. ''et al.'' Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. ''Sci Rep'' '''5''', 14567 (2015). https://doi.org/10.1038/srep14567. </ref>. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens.

== Global Methane Hub Metadata ==
{| class="wikitable"
|'''Origin:'''
|Leibniz Institute DSMZ, Germany
|-
|'''Sequenced by:'''
|Plasmidsaurus, ONT sequencing
|-
|'''Assembled by:'''
|Christian Heryakusuma
|-
|'''Methylome called by:'''
|William G. Alexander
|-
|'''Methyltransferases cloned by:'''
|Guss Lab, ORNL
|-
|'''MIC and Culturing Conditions by:'''
|Christian Heryakusuma
|-
|'''Transformation by:'''
|
|}
'''''Abbreviation:''''' ONT, Oxford Nanopore Technologies; ORNL, Oak Ridge National Laboratory.

== Genome ==
{| class="wikitable" style="float: left; margin-right: 2em;"
|+
! colspan="2" |Assembly Summary
|-
|Completeness
|99.97%
|-
|Contamination
|0.16%
|-
|Total contigs
|1
|-
|Max contig length
|1,887,794 bp
|-
|GC content
|30.07%
|}
{| class="wikitable" style="float: left;"
|+
! colspan="2" |Annotation Summary
|-
|Coding density
|88.1%
|-
|tRNAs
|33
|-
|tmRNAs
|0
|-
|rRNAs
|7
|-
|ncRNAs
|1
|-
|ncRNAs regions
|1
|-
|CRISPR arrays
|0
|-
|CDSs
|1847
|-
|Pseudogenes
|2
|-
|Hypotheticals
|1585
|-
|sORFs
|0
|-
|Gaps
|0
|-
|oriCs
|0
|-
|oriVs
|0
|-
|oriTs
|0
|}
<div style="clear: both;"></div>

Genomic DNA (gDNA) of ''M. gottschalkii'' HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch® Spin gDNA Extraction Kit following manufacturer protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with phage pseudomurein endoisopeptidase of ''Methanocatella smithii'' PS (PeiS); an ''Escherichia coli'' strain encoding the PeiS gene was kindly provided by Prof. Metcalf (University of Illinois Urbana-Champaign).

The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.

== Methylome ==

=== Methylation pattern ===
{| class="wikitable"
|+
|'''#motif'''
|'''methylCounts'''
|'''totalCounts'''
|'''%motifsMethyl'''
|-
|C(6mA)YNNNNNRTTG
| align="right" |1495
| align="right" |1558
| align="right" |95.96
|-
|CA(6mA)YNNNNNRTG
| align="right" |1522
| align="right" |1558
| align="right" |97.69
|}
Methylation motifs were analyzed using MIJAMP<ref>Alyssa K Tidwell, Evelyn Faust, Carrie A Eckert, Adam M Guss, William G Alexander, Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP, ''Journal of Industrial Microbiology and Biotechnology'', Volume 52, 2025, kuaf022, https://doi.org/10.1093/jimb/kuaf022. </ref>. 4mC and 5mC motifs were not present in this isolate.

=== DefenseFinder Results ===
add here

=== Methylating ''E. coli'' ===
''E. coli'' strain AG21365 developed by ORNL was used as a host to generate plasmids with ''M. gottschalkii'' HO methylation motifs shown above.

== Culturing Conditions ==
''M. gottschalkii'' HO is cultivated in GMH-VT2 medium at 37°C and 50 rpm with a 30 psig gas mixture of H2:CO2 (80:20, v/v) as an energy substrate. Growth is typically observed within 24 to 48 h. This methanogen can also be cultivated on GMH-VT2 plates using 1.5% gelrite or 2% agar as a gelling agent with a 12 to 30 psig H2:CO2 (80:20, v/v) gas mixture as an energy substrate. Visible growth on plate is usually observable within 2 to 5 days. The viability of ''M. gottschalkii'' HO on agar plates is 10-30 times higher than that of those grown on gelrite plates.

== Antimicrobial MIC Tests ==
[[File:Antimicrobial MIC Tests - M. gottschalkii HO.png|thumb|395x395px|Antimicrobial susceptibility tests on ''M. gottschalkii'' HO'''. Source:''' Christian Heryakusuma.]]

{| class="wikitable"
|+
! rowspan="2" |Antibiotics
! colspan="2" |Concentration
! rowspan="2" |Observation Period
|-
!style="text-align: center;" |'''Liquid'''
!style="text-align: center;" |'''Solid'''
|-
|Sodium sulfite
|0.5 mM
|0.3 mM
|style="text-align: center;" | ~240 h
|-
|Mevinolin
|40 μM
|20 μM
|style="text-align: center;" | ~240 h
|-
|5-fluoroorotic acid (5-FOA)
|style="color: red;"| ''Insensitive''
|style="color: red;"| ''Insensitive''
|style="text-align: center;" | ~240 h
|-
|8-azahypoxanthine (8-AH)
|style="color: red;"| ''Insensitive''
|style="color: red;"| ''Insensitive''
|style="text-align: center;" | ~240 h
|-
|6-mercaptopurine (6-MP)
|style="color: red;"| ''Insensitive''
|style="color: red;"| ''Insensitive''
|style="text-align: center;" | ~240 h
|-
|5-fluorouracil (5-FU)
|0.25 mg/mL
|0.15 mg/mL
|style="text-align: center;" | ~240 h
|-
|Sodium 2-bromoethanesulfonate (BES)
|2 mM
|1 mM
|style="text-align: center;" | ~240 h
|}

Susceptibility testing was evaluated in GMH-VT2 medium inoculated with a 4% ''M. gottschalkii'' HO culture that has a starting OD600 of ~0.4. ''M. gottschalkii'' HO was considered sensitive to the selection or counterselection agents if there was no increase in the OD600 during the ~240 h (10 days) observation period.

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==